Graph Node Embeddings Embedding Tools

Tools for learning vector representations of nodes and graphs through unsupervised or self-supervised methods. Includes multi-scale embeddings, domain-specific graph embedding techniques (roads, stations, GO terms), and graph classification via embeddings. Does NOT include general graph neural networks, knowledge graph embeddings, or downstream task applications like drug discovery or influence maximization.

There are 55 graph node embeddings tools tracked. 4 score above 50 (established tier). The highest-rated is eliorc/node2vec at 62/100 with 1,293 stars.

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#	Tool	Score	Tier	Stars	Language
1	eliorc/node2vec Implementation of the node2vec algorithm.	62	Established	1,293	Python
2	mims-harvard/decagon Graph convolutional neural network for multirelational link prediction	51	Established	469	Jupyter Notebook
3	mims-harvard/nimfa Nimfa: Nonnegative matrix factorization in Python	51	Established	557	Python
4	ferencberes/online-node2vec Node Embeddings in Dynamic Graphs	51	Established	57	Jupyter Notebook
5	claws-lab/jodie A PyTorch implementation of ACM SIGKDD 2019 paper "Predicting Dynamic...	49	Emerging	414	Python
6	mims-harvard/Raindrop Graph Neural Networks for Irregular Time Series	48	Emerging	219	Python
7	dawenl/cofactor CoFactor: Regularizing Matrix Factorization with Item Co-occurrence	48	Emerging	166	Jupyter Notebook
8	mims-harvard/graphml-tutorials Tutorials for Machine Learning on Graphs	48	Emerging	230	Jupyter Notebook
9	mims-harvard/scikit-fusion scikit-fusion: Data fusion via collective latent factor models	47	Emerging	151	Python
10	abojchevski/graph2gauss Gaussian node embeddings. Implementation of "Deep Gaussian Embedding of...	47	Emerging	179	Python
11	eugeneyan/ml-surveys 📋 Survey papers summarizing advances in deep learning, NLP, CV, graphs,...	46	Emerging	2,881	—
12	mims-harvard/SubGNN Subgraph Neural Networks (NeurIPS 2020)	46	Emerging	202	Python
13	mims-harvard/GraphXAI GraphXAI: Resource to support the development and evaluation of GNN explainers	46	Emerging	206	Python
14	sashakolpakov/graphem-rapids Graph embedding for influence maximization in networks	45	Emerging	4	Python
15	snash4/GAT2VEC embedding attributed graphs	44	Emerging	57	Python
16	neo4j-product-examples/graph-machine-learning-examples Neo4j Graph Data Science with Graph ML & GNNs	43	Emerging	47	Jupyter Notebook
17	xgfs/verse Reference implementation of the paper VERSE: Versatile Graph Embeddings from...	43	Emerging	134	C++
18	rodrigo-arenas/Graph-Embeddings Graph and Nodes embeddings for downstream tasks	42	Emerging	5	Python
19	pedugnat/dynnode2vec dynnode2vec is a python package that implements algorithms to embed dynamic graphs	41	Emerging	12	Python
20	uhh-lt/path2vec Learning to represent shortest paths and other graph-based measures of node...	41	Emerging	33	Jupyter Notebook
21	nate-russell/Network-Embedding-Resources Network Embedding Survey and Resources	40	Emerging	41	—
22	benedekrozemberczki/diff2vec Reference implementation of Diffusion2Vec (Complenet 2018) built on Gensim...	40	Emerging	127	Python
23	aedera/anc2vec Unsupervised neural network for learning embeddings of GO terms.	39	Emerging	21	Python
24	HKUST-KnowComp/SRBRW Source Code for IJCAI 2018 paper "Biased Random Walk based Social...	37	Emerging	9	C
25	talshapira/BGP2Vec We introduce a novel approach for Autonomous System (AS) embedding using...	36	Emerging	9	Jupyter Notebook
26	bio-ontology-research-group/DL2Vec Convert Description Logic axioms into a graph, and generate embedding...	34	Emerging	19	Python
27	aida-ugent/DeBayes DeBayes: a Bayesian Method for Debiasing Network Embeddings (ICML 2020).	33	Emerging	8	Python
28	OlegDurandin/dtree2vec This project contain implementation the system, proposed in the "Adapting...	32	Emerging	3	HTML
29	specialprocedures/semnet Semnet efficiently constructs graph structures from embeddings, enabling...	32	Emerging	5	Python
30	vedashree29296/PyEmbeo graph embeddings for neo4j in python	31	Emerging	27	Python
31	Calychas/highway2vec highway2vec: representing OpenStreetMap microregions with respect to their...	31	Emerging	4	Jupyter Notebook
32	mims-harvard/fastGNMF Fast graph-regularized matrix factorization	29	Experimental	20	Python
33	joisino/gnnrecover Code for "Graph Neural Networks can Recover the Hidden Features Solely from...	29	Experimental	24	Python
34	sayalaruano/DengueDrugRep A project to predict new repurposed drugs for dengue using a biomedical...	29	Experimental	3	Jupyter Notebook
35	pietrocinaglia/dante DANTE is a software tool for pairwise alignment of dynamic networks. It...	29	Experimental	1	—
36	GemsLab/RGM Fast embedding-based graph classification with connections to kernels	28	Experimental	13	Python
37	arangoml/fastgraphml Given an input graph (ArangoDB or PyG) it generates graph embeddings using...	27	Experimental	68	Python
38	meowoodie/Regularized-RBM A regularized version of RBM for unsupervised feature selection.	24	Experimental	13	Python
39	FOCS-AI/linkwise Topology-Driven Edge Predictions with Graph Machine Learning for Optical...	22	Experimental	2	Jupyter Notebook
40	ErikLundin98/hermitian_laplacian_graph Node embedding extraction using GraphWave and the Hermitian Laplacian	22	Experimental	2	Jupyter Notebook
41	GemsLab/EMBER Node embedding for directed, weighted networks	21	Experimental	7	Python
42	shan1322/Hyperwalk embeddings for hyperedges in a hypergraph	21	Experimental	7	Python
43	SmartData-Polito/gnn-for-darknet This repo contains the codes and the notebooks used for the paper "Exploring...	20	Experimental	8	Jupyter Notebook
44	monomonedula/sten Simple algorithm for generating graph nodes embeddings	20	Experimental	6	Python
45	kevinbdsouza/graph_embed_hic SCI and LINE to form Hi-C graph embeddings. Comparison with Hi-C-LSTM....	19	Experimental	3	Python
46	SelimWaly/Neural-Network-Graph-Learning SDNE and LINE Deep Learning Graph Embeddings Implementation	19	Experimental	3	Jupyter Notebook
47	RMilock/multi-scale-node-embeddings Official repository for the paper "Multi-Scale Node Embeddings for Graph...	17	Experimental	—	Python
48	pyvandenbussche/node2vec-arxiv Experiment using node2vec on arxiv papers metadata	17	Experimental	1	Python
49	Birunda3000/GNNs_X_GAE-S_cla Repositório de TCC com pipeline completo para experimentos com GNNs: geração...	13	Experimental	—	Python
50	OxfordRSE/L2Gv2 Infer global embeddings from local graph embeddings	13	Experimental	—	Python
51	atsushi-green/station2vec learning station embedding	11	Experimental	—	Python
52	MIND-Lab/DAGE Deep Attributed Graph Embedding	11	Experimental	4	Python
53	tteofili/parse2vec NLP tool to enrich word embeddings with parse tree information and generate...	11	Experimental	—	Java
54	merklefruit/hpc2020-graphML My submission for the HPC GraphML contest by Oracle Labs and NECSTLab at...	11	Experimental	—	Jupyter Notebook
55	ImmanuelSandeep/Drug-Drug-Interaction-Prediction This project presents a Graph Neural Network (GNN)-based framework for...	10	Experimental	1	Jupyter Notebook

Comparisons in this category

online-node2vec and dynnode2vec (51 vs 41)